[PyMOL] lcd stereo

I just noticed that the price on the Sharp LCD stereo monitor is now $600. http://store.sharpsystems.com/product.asp?sku=2555920 Is it possible to run pymol on linux in stereo on this?

[PyMOL] Re: Apple's tk and pymol

I just fired up pymol installed via fink using Python compiled against a Framework build of Python that in turn is build against the TCL TK framework. your either get interaction with the GLUT GUI, or the Tcl/Tk user interface, but not both : (. I can't reproduce the problem, i.e., both gu

RE: [PyMOL] Re: Apple's tk and pymol

Hi Warren: The display window is actually X so I assume it must be fink/X11 glut. Sorry I omitted that. Bill > > Are you using Framework GLUT or Fink/Xll GLUT? The latter might work >

[PyMOL] pymol -M ?

Hi Mark: I just tried the command with -M and it didn't help, but for the record, you can use /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL or if you are a nerd, you might prefer this shell script, which you can call pymol and put in your $path array. It finds wherever you put it

[PyMOL] apbs and pymol in fink (OS X)

I have the same problem on a mac G5 dual processor with newly compiled pymol 0.98 and apbs 3.2, installed by fink. Also occurs with the standalone mac/xll hybrid executable, calling apbs 3.2 using the plug in menu. Interestingly, the programs work fine together on my mac G4 laptop, with singl

[PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

I'm not getting very far... parsePBE: Warning -- parsed deprecated "calcforce 0" statement. parsePBE: Please use "calcforce no" instead. PBEparm_check: SDENS not set! NOsh: MG parameters not set correctly! Error while parsing input file.

Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

s > -Torrence, Bring It On| / \ | mler...@umich > > On Tue, 20 Dec 2005, William Scott wrote: > > > I'm not getting very far... > > > > parsePBE: Warning -- parsed deprecated "calcforce 0" statement. > > parsePBE: Please

[PyMOL] Re: PymolX11Hybrid problems (Avram Slovic)

> > I am having a hard time getting PymolX11Hybrid properly installed on > my G4 powerbook. My goal is to make molecular surfaces with > elctrostatic potentials. What am I doing wrong? I installed the > newest version of MacPymol, duplicated it, renamed it > PymolX11Hybrid. Then I downloaded the

[PyMOL] Re: electrostatic potential of nucleic acids possible in pyMOL?

Yes. In fact I just added a description of how to do this in the PyMol Wiki. http://www.pymolwiki.org/index.php/APBS The apbs plugin will work , but you should use pdb2pqr to generate the nucleic acid pqr file externally, and then read it in. Then it works the same as for proteins. HTH, Bill

[PyMOL] Re: invoking pymol the unix way on os x

You can call the executable inside an application and it will work in the normal unix way, eg /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL You might want to make an alias or a function or a symbolic link like alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL or pymol(

[PyMOL] stereo and intel macs

Does anyone know if the new intel min-macs support stereo, either by default or after being fitted with an appropriate video card? The idea of chucking my O2s and replacing them with mini-macs is quite appealing... Thanks. Bill Scott

[PyMOL] libnvidia-tls.so.1: cannot handle TLS data

Hi: I'm running pymol on Ubuntu with ubuntu's nvidia driver. I get the error libnvidia-tls.so.1: cannot handle TLS data upon startup. If I move the directory /usr/lib/tls out of the way, pymol works, but then upon reboot, my display is blank. Any suggestions? Bill PS: I just noticed that

RE: [PyMOL] libnvidia-tls.so.1: cannot handle TLS data

...@lists.sourceforge.net] On Behalf Of William Scott Sent: Friday, April 07, 2006 11:52 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] libnvidia-tls.so.1: cannot handle TLS data Hi: I'm running pymol on Ubuntu with ubuntu's nvidia driver. I get the error libnvidia-tls.so

[PyMOL] libnvidia-tls.so.1: cannot handle TLS data

Hi folks: I've just compiled the most recent pymol on Ubuntu 5.10 with ubuntu's nvidia driver. I (still) get the error libnvidia-tls.so.1: cannot handle TLS data upon startup. If I move the directory /usr/lib/tls out of the way, pymol then works, but then upon reboot, my display is bla

Re: [PyMOL] PyMol question?

Hi Mark: Most likely there is, but I don't know the answer to your question. I'm posting this to the pymol users list (via cc) so hopefully someone else will know the answer. I trust all is going well for you. Bill On Jun 30, 2006, at 8:19 AM, Mark Collins wrote: Hi Bill, I've been lo

[PyMOL] cartoon question

Hi folks: I have a closed covalent circle of RNA that I want to represent with a cartoon in pymol, and there is a discontinuity at the phosphodiester bond between residue 1 and residue N. Is there a way to make a smooth closed circular phosphodiester backbone? Thanks. Bill William G. Sc

[PyMOL] I need a new graphics card

Hi folks: Somehow we roached a graphics card on my G4 (it is about 3 years old, dual 1.25 GHz processors, don't remember the video card). Is it possible to put one of the Apple stereo-compatible ones in its place? Thanks. Bill

Re: [PyMOL] Pymol cone shape?

s can do it. Oh well, .. On Wed, 10 Jan 2007, William Scott wrote: I think it is possible, but I don't know how. On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: Hi Bill, is it possible to draw a cone-shape in pymol?

[PyMOL] 3d pdf

Is it possible to create a 3D pdf using pymol? William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/

Re: [PyMOL] 3d pdf

space. Something similar may be of use to you. > If you want, I can send you the program, or a script which does a > similar thing. Alternatively, I can just send the routine to write an > xplor map, given a 3D array (C code, though maybe I already have it in > python too). > >

[PyMOL] svn 1.0r2?

Is there a way to get the current (is it 1.0r2?) svn pymol? What I am using currently has a problem in which the tcltk menu freezes after I use the pdb download plugin. Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/

Re: [PyMOL] How do I handle pmw virtual package for pymol 1.0 on Mac OS 10.4.10?

Hi Lorraine: All of the python packages in fink have suffixes that correspond to version numbers, so if you wanted to use pymol with the most current python, you should issue fink selfupdate; fink update-all; fink install pymol-py25 I would have thought that would automatically ensure you ha

Re: [PyMOL] How do I handle pmw virtual package for pymol 1.0 on Mac OS 10.4.10?

hat you are far better off to move aside your /sw > directory and reinstall the current fink in that case. > Jack > > ----- Original Message - > From: William Scott > Date: Wednesday, September 19, 2007 10:37 am > Subject: Re: [PyMOL] How do I handle pm

Re: [PyMOL] COVER image

'turn z, 270' (sorry) On Tue, 20 Nov 2007, Vincent Chaptal wrote: Hello, I am trying to make a picture for a cover and I am wondering how to make a vertical image. (Pymol creates horizontal images, and journal covers are vertical) Is there a way to creates those

Re: [PyMOL] Pymol Crash in X11 on MacOSX 10.5

I've noticed after updating to X11 2.1.3 that X11 crashes reproducibly if I (for example) resize coot's window before it finishes loading. I don't recall having X11 crash ever with 2.1.1 or earlier. Fortuitiously, the 10.5.2 update reverts X11 to 2.1.1, so updating that might solve the problem

[PyMOL] PyMol fruit-menu incompatability on OS X

Hi: I've noticed that the performance of pymol on my laptop after an OS X upgrade to 10.2 (and corresponding pymol 0.84 upgrade) was much worse. Although I think 10.2.1 is definitely slower and more buggy than 10.1.5, I tracked down the main culprit: A $7 piece of shareware called Fruit Men

[PyMOL] fink python woes

Hi, Anybody know what this message is caused by? [chem05:~] grayt% pymol Traceback (most recent call last): File "/sw/lib/pymol/modules/pymol/__init__.py", line 59, in ? import threading File "/sw/lib/python2.2/threading.py", line 4, in ? import time ImportError: No

[PyMOL] Auto-launching in Mac Terminal

Actually, I've encountered this problem myself -- very annoying... What happened is that you saved the Terminal window settings while you had a PyMOL session open, so OS X inferred that you were indicating a desire to have PyMOL open as a default preference. The only way I know of changing this

[PyMOL] How do I auto-load my startup pymol script in the new os x version?

Hi folks: I just installed the new pymol 0.91 for os x. I used to start pymol this way: alias pymol "/Applications/PyMOL/Darwin/pymol.com -q /Users/wgscott/pymol/alias.pml" Now that option appears to be gone, so I tried alias pymol "open -a /Applications/PyMOL.app /Users/wgscott/pymol/al

[PyMOL] Powermate dial with Pymol on OS X

Hi folks: I'd like to use my Powermate(TM) dial on OS X with Pymol. It works great with O and other programs. In essence, you can tell it to issue a keystroke when you turn the dial. At first, I thought I would try this: alias y, rotate y,0.1 Then I can program the stupid driver to issue a

Re: [PyMOL] Powermate dial with Pymol on OS X

Thanks, Ezequiel! That is exactly what I needed. I guess I need to RTFM some more... So for anyone else who might be interested, here is how to get the Powermate dial to play nice with Pymol (I did this on OS X but I assume it would be very similar on Windows). http://chemistry.ucsc.edu/~wg

[PyMOL] Powermate dial

Hi Nat: I am really impressed with Zac's driver and extension, and I probably should get a multi-button trackball. For now, the simplicity (or limitation) of the dial (turn right, turn left, press-while-turning right/left, short click, long click) can be augmented to give some flexibility.

[PyMOL] superposition of two molecules

This is driving me nuts. I am trying to superimpose two RNA molecules: PyMOL>load trna10.pdb Executive: object "trna10" created. PyMOL>load ref4.pdb Executive: object "ref4" created. PyMOL>color blue Executive: Colored 2668 atoms. PyMOL>color yellow, ( trna10 and resid 10:15 and na

[PyMOL] Re: PyMOL-APBS os x

The best way to overcome this is to compile it, so that you don't have to depend on someone's dynamic library. Fink doesn't build the g77 dynamic library, which allows you to avoid this problem. If you use g77 3.4.1 (which is what is currently in fink) with gcc 3.3 you will have some linkin

[PyMOL] compiling maloc and apbs on os x -- fink info scripts

Hi Jianghai et al: Hopefully these will make someone's life easier: Here is an info file for maloc: http://www.chemistry.ucsc.edu/%7Ewgscott/fink/info/maloc.info Drop this into /sw/fink/dists/local/main/finkinfo and issue fink install maloc Here is one for apbs: http://www.chemistry.

[PyMOL] pymol and OS X v. 10.3.5 update -- a word of caution

Hi Folks: I did the Mac OS X update to v. 10.3.5 yesterday and this changes some graphics card software. PyMOL now exhibits a really annoying flickering in rock mode, especially evident when electron density is being displayed. I don't know if this is peculiar to my system but if you are c

[PyMOL] Re: [ccp4bb]: pymol and OS X v. 10.3.5 update -- a word of caution

Here is the one that is giving me problems: What Mac generation are you using, and what video card specifically? GeForce4 Ti 4600 Machine Model:Power Mac G4 CPU Type: PowerPC G4 (3.2) Number Of CPUs: 2 CPU Speed:1.25 GHz L2 Cache (per CPU): 256 KB L3 Cach

[PyMOL] an updated fink version of pymol for os x v. 10.3.x

Hi Folks: Thanks to the efforts of Jack Howarth, who has volunteered to maintain the pymol package in fink, we now have an up-to-date version 0.97 of the x-windows pymol in the 10.3 unstable branch of fink (or will as soon as cvs updates it -- usually within 24 hours or fewer). If you don't

[PyMOL] OS X users: fink install scripts for apbs and maloc

Hi folks: I was alerted to the fact that I made a mistake in my original fink install scripts for apbs and its dependency called maloc. The corrected ones are here: http://chemistry.ucsc.edu/%7Ewgscott/fink/info/apbs.info http://chemistry.ucsc.edu/%7Ewgscott/fink/info/maloc.info I can't put

[PyMOL] maps and asymmetric units

On Tue, 28 Sep 2004 pymol-users-requ...@lists.sourceforge.net wrote: > From: Jacob Corn > To: pymol-users > Subject: [PyMOL] reiterating a ccp4 map problem > > I have several CCP4 maps that have been calculated over the entire unit > cell (using ccp4's "extend") that can be read in, but only dis

[PyMOL] MacPyMOL startup question

I have my pdb files set to open up by default with MacPyMOL. Is there a command I can put into .pymolrc or somewhere to cd to the dirname of the file that I clicked on? Right now the pwd is the /Applications folder, which means stuff saves to the wrong place by default. Did cd $PWD used to work,

[PyMOL] Re: Map Origin and PDB (surendra negi)

Since you have ccp4, you can use mapmask: #!/bin/sh # Extend to cover the molecule mapmask mapin yourmap.ccp4 xyzin yourmodel.pdb mapout newmap.ccp4 << eof BORDER 5.0 MODE mapin eof

[PyMOL] Re: PyMOL for screen on OS X

I find maximizing the screen with the green button works fine with virtual desktops and has the added merit of keeping the title bar menu items accessible. I wish there was a way of making that the default behavior (I seem to remember that it used to be). HTH, Bill

[PyMOL] G5 and pymol flashing

Hi folks: I bought a new G5 fairly recently. When using pymol, the screen goes white for brief instances when rotating a molecule, giving rise to a flashing effect that is so off-putting it keeps me from using pymol on this machine. I have a 20" monitor and the following video card: PCI/AG

[PyMOL] DNA builder

The Namot program is free: http://namot.lanl.gov/ It's pdb format it outputs is a bit delusional. This is a shell script I wrote to fix it up (relies on having CNS): http://babyurl.com/DpdVJe HTH, Bill

[PyMOL] aqual tcltk Pmw gui

15 May 2005 16:14:07 +0100 To: William Scott , fink-de...@lists.sourceforge.net Dear Fink Developers, Pymol's install plugin menu gives the following error: AttributeError Exception in Tk callback Function: at 0x56d0cf0> (type: 'function'>) Args: () Traceback (inne

[PyMOL] Fwd: aqual tcltk Pmw gui: I was wrong

brary/Frameworks/Python.framework/Versions/Current/lib/ python2.3/ Sorry. Bill Begin forwarded message: From: William Scott Date: May 16, 2005 7:51:28 AM PDT To: Murali Vadivelu Cc: fink-de...@lists.sourceforge.net, pymol- us...@lists.sourceforge.net Subject: aqual tcltk Pmw gui Reply-To:

[PyMOL] keynote and pymol

> > I was wondering if anyone out there has any experiance with usuing Apple's > Keynote to display animated pymol gif's. I've had a look in the archives and > couldn't find anything. > > On a second note (and sorry to open up this debate again), What is the > consensus for displaying a pymol mo